Despite the utility of the mouse and other non-primate vertebrates in studying human lipid metabolism, many human metabolic features are best modeled in primates, particularly our response to dietary cholesterol. The differential regulation of genes involved in cholesterol homeostasis in humans and mice is believed to significantly contribute to differences in response to dietary cholesterol between these species. We have previously shown that sequence comparisons of multiple primate species are successful at identifying functional elements specific to primates and complement traditional sequence comparisons with non-primate mammals, such as between human and mouse. Accordingly, the goal of this proposal is to couple multiple primate sequence comparisons with functional studies to discover primate-specific regulatory elements impacting on lipid metabolism. This will include the analysis of several genes participating in lipid metabolism, with an emphasis on the dissection of the transcriptional network of the nuclear hormone receptor LXR-a and its target genes, crucial regulators of cholesterol homeostasis which appear to have differential regulation in human and mouse. We will: 1) identify and functionally characterize regulatory sequences preferentially conserved in the primate lineage through the comparative analysis of large genomic intervals containing known "lipid" genes;2) identify and functionally characterize primate specific transcription factor binding sites in both known and computationally predicted regulatory elements shared between primates and non-primate mammals;and 3) investigate the function of primate-specific regulatory sequences on their neighboring human genes in cell culture and in vivo studies and determine their contribution to primate-specific phenotypes. These studies will provide genomically derived insights into the clinically relevant regulation of cholesterol homeostasis and contribute to our understanding of primate-specific responses to environmental stimuli. The mouse, while a valuable model of human diseases such as plasma lipid disorders leading to atherosclerosis, has many differences from human, with the immediate consequence that many drugs first tested successfully in mice fail in later clinical studies in humans. In this proposal, we plan to identify segments of the human genome which determine differences in plasma lipid metabolism between human and mouse. Discovery of this kind of molecular genomic structures will shed new light into the pathogenic mechanisms leading to human lipid disorders, promising to lead to the engineering of better mouse models for this important human disease.